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brentp / slivar

genetic variant expressions, annotation, and filtering for great good.
MIT License
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slivar tsv: extract QUAL and FORMAT fields #104

Closed Madelinehazel closed 2 years ago

Madelinehazel commented 2 years ago

Hello, Is there any way to extract the QUAL field for each variant, as well as the alternate allele depths for each sample when using slivar tsv?

Thanks, Madeline

brentp commented 2 years ago

Hi, you can derive the AD allele depths using DP *AB which are output for each sample. For qual, you can't get that currently. I'll add it for next release. -B

Madelinehazel commented 2 years ago

Awesome, thanks Brent!

Madelinehazel commented 2 years ago

(Any estimates as to a timeline for next release?)

brentp commented 2 years ago

If you'll try this attached binary and verify it works for you, I can get a new release out this week. (You'll know you have the right version in your path as it will show v0.2.6 when run without args.) slivar.gz

brentp commented 2 years ago

This will be available in release in the next week, you can get the QUAL as:

slivar tsv -i QUAL
justme66 commented 4 months ago

Hi Brent, Is there any way I can get GQ for each variant? Can I modify the 'src/slivarpkg/tsv.nim' and create binary slivar by myself to get GQ or other info for each variant?

Thanks, Emma

brentp commented 4 months ago

@justme66 , yes, that's possible. you could write a getGQ function copying from getAB and getDP and then also see the call-site for those functions.

justme66 commented 4 months ago

Thank you. Brent.